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        <a href="weblogolib-module.html">Package&nbsp;weblogolib</a> ::
        Module&nbsp;_cli
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<h1 class="epydoc">Source Code for <a href="weblogolib._cli-module.html">Module weblogolib._cli</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment">#!/usr/bin/env python</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-comment"># -------------------------------- WebLogo --------------------------------</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-comment">#  Copyright (c) 2003-2004 The Regents of the University of California.</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  Copyright (c) 2005 Gavin E. Crooks</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  Copyright (c) 2006-2011, The Regents of the University of California, through </tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  Lawrence Berkeley National Laboratory (subject to receipt of any required</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  approvals from the U.S. Dept. of Energy).  All rights reserved.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-comment">#  This software is distributed under the new BSD Open Source License.</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  &lt;http://www.opensource.org/licenses/bsd-license.html&gt;</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  Redistribution and use in source and binary forms, with or without </tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  modification, are permitted provided that the following conditions are met: </tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  (1) Redistributions of source code must retain the above copyright notice, </tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  this list of conditions and the following disclaimer. </tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  (2) Redistributions in binary form must reproduce the above copyright </tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  notice, this list of conditions and the following disclaimer in the </tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  documentation and or other materials provided with the distribution. </tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  (3) Neither the name of the University of California, Lawrence Berkeley </tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  National Laboratory, U.S. Dept. of Energy nor the names of its contributors </tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  may be used to endorse or promote products derived from this software </tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  without specific prior written permission. </tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" </tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE </tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE </tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE </tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR </tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF </tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS </tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN </tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) </tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE </tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#  POSSIBILITY OF SUCH DAMAGE. </tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line"><tt class="py-comment"># WebLogo Command Line Interface</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Module weblogolib.color=weblogolib.color-module.html,Method weblogolib.colorscheme.ColorScheme.color()=weblogolib.colorscheme.ColorScheme-class.html#color"><a title="weblogolib.color
weblogolib.colorscheme.ColorScheme.color" class="py-name" href="#" onclick="return doclink('link-0', 'color', 'link-0');">color</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Module weblogolib.colorscheme=weblogolib.colorscheme-module.html"><a title="weblogolib.colorscheme" class="py-name" href="#" onclick="return doclink('link-1', 'colorscheme', 'link-1');">colorscheme</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Class weblogolib.colorscheme.ColorScheme=weblogolib.colorscheme.ColorScheme-class.html"><a title="weblogolib.colorscheme.ColorScheme" class="py-name" href="#" onclick="return doclink('link-2', 'ColorScheme', 'link-2');">ColorScheme</a></tt><tt class="py-op">,</tt> <tt id="link-3" class="py-name" targets="Class weblogolib.colorscheme.ColorGroup=weblogolib.colorscheme.ColorGroup-class.html"><a title="weblogolib.colorscheme.ColorGroup" class="py-name" href="#" onclick="return doclink('link-3', 'ColorGroup', 'link-3');">ColorGroup</a></tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">corebio</tt><tt class="py-op">.</tt><tt class="py-name">utils</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">string</tt> <tt class="py-keyword">import</tt> <tt class="py-name">Template</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">corebio</tt> <tt class="py-keyword">import</tt> <tt class="py-name">seq_io</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line"> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt>  </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">corebio</tt><tt class="py-op">.</tt><tt class="py-name">utils</tt><tt class="py-op">.</tt><tt class="py-name">deoptparse</tt> <tt class="py-keyword">import</tt> <tt class="py-name">DeOptionParser</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">optparse</tt> <tt class="py-keyword">import</tt> <tt class="py-name">OptionGroup</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line"> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name" targets="Package weblogolib=weblogolib-module.html"><a title="weblogolib" class="py-name" href="#" onclick="return doclink('link-4', 'weblogolib', 'link-4');">weblogolib</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Class weblogolib.LogoOptions=weblogolib.LogoOptions-class.html"><a title="weblogolib.LogoOptions" class="py-name" href="#" onclick="return doclink('link-5', 'LogoOptions', 'link-5');">LogoOptions</a></tt><tt class="py-op">,</tt> <tt id="link-6" class="py-name" targets="Class weblogolib.LogoData=weblogolib.LogoData-class.html"><a title="weblogolib.LogoData" class="py-name" href="#" onclick="return doclink('link-6', 'LogoData', 'link-6');">LogoData</a></tt><tt class="py-op">,</tt> <tt id="link-7" class="py-name" targets="Class weblogolib.LogoFormat=weblogolib.LogoFormat-class.html"><a title="weblogolib.LogoFormat" class="py-name" href="#" onclick="return doclink('link-7', 'LogoFormat', 'link-7');">LogoFormat</a></tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-8" class="py-name"><a title="weblogolib" class="py-name" href="#" onclick="return doclink('link-8', 'weblogolib', 'link-4');">weblogolib</a></tt> <tt class="py-keyword">import</tt> <tt class="py-name">parse_prior</tt><tt class="py-op">,</tt> <tt id="link-9" class="py-name" targets="Variable weblogolib.description=weblogolib-module.html#description"><a title="weblogolib.description" class="py-name" href="#" onclick="return doclink('link-9', 'description', 'link-9');">description</a></tt><tt class="py-op">,</tt> <tt id="link-10" class="py-name" targets="Variable weblogolib.release_description=weblogolib-module.html#release_description"><a title="weblogolib.release_description" class="py-name" href="#" onclick="return doclink('link-10', 'release_description', 'link-10');">release_description</a></tt><tt class="py-op">,</tt> <tt id="link-11" class="py-name" targets="Variable weblogolib.formatters=weblogolib-module.html#formatters"><a title="weblogolib.formatters" class="py-name" href="#" onclick="return doclink('link-11', 'formatters', 'link-11');">formatters</a></tt><tt class="py-op">,</tt> <tt class="py-name">default_formatter</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-12" class="py-name"><a title="weblogolib" class="py-name" href="#" onclick="return doclink('link-12', 'weblogolib', 'link-4');">weblogolib</a></tt> <tt class="py-keyword">import</tt> <tt id="link-13" class="py-name" targets="Variable weblogolib.std_alphabets=weblogolib-module.html#std_alphabets"><a title="weblogolib.std_alphabets" class="py-name" href="#" onclick="return doclink('link-13', 'std_alphabets', 'link-13');">std_alphabets</a></tt><tt class="py-op">,</tt> <tt id="link-14" class="py-name" targets="Variable weblogolib.std_units=weblogolib-module.html#std_units"><a title="weblogolib.std_units" class="py-name" href="#" onclick="return doclink('link-14', 'std_units', 'link-14');">std_units</a></tt><tt class="py-op">,</tt> <tt id="link-15" class="py-name" targets="Variable weblogolib.std_sizes=weblogolib-module.html#std_sizes"><a title="weblogolib.std_sizes" class="py-name" href="#" onclick="return doclink('link-15', 'std_sizes', 'link-15');">std_sizes</a></tt><tt class="py-op">,</tt> <tt id="link-16" class="py-name" targets="Variable weblogolib.std_color_schemes=weblogolib-module.html#std_color_schemes"><a title="weblogolib.std_color_schemes" class="py-name" href="#" onclick="return doclink('link-16', 'std_color_schemes', 'link-16');">std_color_schemes</a></tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-17" class="py-name"><a title="weblogolib" class="py-name" href="#" onclick="return doclink('link-17', 'weblogolib', 'link-4');">weblogolib</a></tt> <tt class="py-keyword">import</tt> <tt id="link-18" class="py-name" targets="Function weblogolib.read_seq_data()=weblogolib-module.html#read_seq_data"><a title="weblogolib.read_seq_data" class="py-name" href="#" onclick="return doclink('link-18', 'read_seq_data', 'link-18');">read_seq_data</a></tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line"> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"><tt class="py-comment"># ====================== Main: Parse Command line =============================</tt> </tt>
<a name="main"></a><div id="main-def"><a name="L64"></a><tt class="py-lineno"> 64</tt> <a class="py-toggle" href="#" id="main-toggle" onclick="return toggle('main');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib._cli-module.html#main">main</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt>  </tt>
</div><a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">    <tt class="py-docstring">"""WebLogo command line interface """</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">     </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">    <tt class="py-comment"># ------ Parse Command line ------</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt class="py-name">_build_option_parser</tt><tt class="py-op">(</tt><tt class="py-op">)</tt>                 </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">    <tt class="py-op">(</tt><tt class="py-name">opts</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt><tt class="py-op">)</tt> <tt class="py-op">=</tt> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">parse_args</tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">args</tt> <tt class="py-op">:</tt> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">error</tt><tt class="py-op">(</tt><tt class="py-string">"Unparsable arguments: %s "</tt> <tt class="py-op">%</tt> <tt class="py-name">args</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">     </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">opts</tt><tt class="py-op">.</tt><tt class="py-name">serve</tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line">        <tt id="link-19" class="py-name" targets="Function weblogolib._cli.httpd_serve_forever()=weblogolib._cli-module.html#httpd_serve_forever"><a title="weblogolib._cli.httpd_serve_forever" class="py-name" href="#" onclick="return doclink('link-19', 'httpd_serve_forever', 'link-19');">httpd_serve_forever</a></tt><tt class="py-op">(</tt><tt class="py-name">opts</tt><tt class="py-op">.</tt><tt class="py-name">port</tt><tt class="py-op">)</tt> <tt class="py-comment"># Never returns?</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">        <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt>  </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">   </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">             </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">    <tt class="py-comment"># ------ Create Logo ------</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">_build_logodata</tt><tt class="py-op">(</tt><tt class="py-name">opts</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">        <tt class="py-name">format</tt> <tt class="py-op">=</tt> <tt class="py-name">_build_logoformat</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">opts</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">         </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">        <tt class="py-name">formatter</tt> <tt class="py-op">=</tt> <tt class="py-name">opts</tt><tt class="py-op">.</tt><tt class="py-name">formatter</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">        <tt class="py-name">formatter</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">format</tt><tt class="py-op">,</tt> <tt class="py-name">opts</tt><tt class="py-op">.</tt><tt class="py-name">fout</tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line"> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">    <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-name">err</tt> <tt class="py-op">:</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">,</tt> <tt class="py-string">'Error:'</tt><tt class="py-op">,</tt> <tt class="py-name">err</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">        <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">    <tt class="py-keyword">except</tt> <tt class="py-name">KeyboardInterrupt</tt><tt class="py-op">,</tt> <tt class="py-name">err</tt><tt class="py-op">:</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">        <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
</div><a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line"><tt class="py-comment"># End main()            </tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line"><tt class="py-comment"></tt>         </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"> </tt>
<a name="httpd_serve_forever"></a><div id="httpd_serve_forever-def"><a name="L93"></a><tt class="py-lineno"> 93</tt> <a class="py-toggle" href="#" id="httpd_serve_forever-toggle" onclick="return toggle('httpd_serve_forever');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib._cli-module.html#httpd_serve_forever">httpd_serve_forever</a><tt class="py-op">(</tt><tt class="py-param">port</tt><tt class="py-op">=</tt><tt class="py-number">8080</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="httpd_serve_forever-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="httpd_serve_forever-expanded"><a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">    <tt class="py-docstring">""" Start a webserver on a local port."""</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">BaseHTTPServer</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">CGIHTTPServer</tt>  </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">     </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">    <tt class="py-keyword">class</tt> <tt class="py-def-name">__HTTPRequestHandler</tt><tt class="py-op">(</tt><tt class="py-base-class">CGIHTTPServer</tt><tt class="py-op">.</tt><tt class="py-base-class">CGIHTTPRequestHandler</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">        <tt class="py-keyword">def</tt> <tt class="py-def-name">is_cgi</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">path</tt> <tt class="py-op">==</tt> <tt class="py-string">"/create.cgi"</tt><tt class="py-op">:</tt>  </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cgi_info</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt><tt class="py-op">,</tt> <tt class="py-string">'create.cgi'</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
</div></div><a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">     </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">    <tt class="py-comment"># Add current directory to PYTHONPATH. This is</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment"># so that we can run the standalone server</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment"># without having to run the install script.      </tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">pythonpath</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">getenv</tt><tt class="py-op">(</tt><tt class="py-string">"PYTHONPATH"</tt><tt class="py-op">,</tt> <tt class="py-string">''</tt><tt class="py-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">    <tt class="py-name">pythonpath</tt> <tt class="py-op">+=</tt> <tt class="py-string">":"</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">abspath</tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">    <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">environ</tt><tt class="py-op">[</tt><tt class="py-string">"PYTHONPATH"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">pythonpath</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line"> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">    <tt class="py-name">htdocs</tt> <tt class="py-op">=</tt> <tt class="py-name">resource_filename</tt><tt class="py-op">(</tt><tt class="py-name">__name__</tt><tt class="py-op">,</tt> <tt class="py-string">'htdocs'</tt><tt class="py-op">,</tt> <tt class="py-name">__file__</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">    <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">chdir</tt><tt class="py-op">(</tt><tt class="py-name">htdocs</tt><tt class="py-op">)</tt>  </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line"> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">    <tt class="py-name">HandlerClass</tt> <tt class="py-op">=</tt> <tt class="py-name">__HTTPRequestHandler</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">    <tt class="py-name">ServerClass</tt> <tt class="py-op">=</tt> <tt class="py-name">BaseHTTPServer</tt><tt class="py-op">.</tt><tt class="py-name">HTTPServer</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">    <tt class="py-name">httpd</tt> <tt class="py-op">=</tt> <tt class="py-name">ServerClass</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">''</tt><tt class="py-op">,</tt> <tt class="py-name">port</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">HandlerClass</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-string">"WebLogo server running at http://localhost:%d/"</tt> <tt class="py-op">%</tt> <tt class="py-name">port</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">     </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">    <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">        <tt class="py-name">httpd</tt><tt class="py-op">.</tt><tt class="py-name">serve_forever</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">    <tt class="py-keyword">except</tt> <tt class="py-name">KeyboardInterrupt</tt><tt class="py-op">:</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">        <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
</div><a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line"><tt class="py-comment"># end httpd_serve_forever()  </tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line"><tt class="py-comment"></tt>     </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">     </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line"> </tt>
<a name="_build_logodata"></a><div id="_build_logodata-def"><a name="L128"></a><tt class="py-lineno">128</tt> <a class="py-toggle" href="#" id="_build_logodata-toggle" onclick="return toggle('_build_logodata');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib._cli-module.html#_build_logodata">_build_logodata</a><tt class="py-op">(</tt><tt class="py-param">options</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="_build_logodata-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_build_logodata-expanded"><a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">     </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">options</tt><tt class="py-op">.</tt><tt class="py-name">input_parser</tt> <tt class="py-op">!=</tt> <tt class="py-string">"transfac"</tt><tt class="py-op">:</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">        <tt class="py-name">seqs</tt> <tt class="py-op">=</tt> <tt id="link-20" class="py-name"><a title="weblogolib.read_seq_data" class="py-name" href="#" onclick="return doclink('link-20', 'read_seq_data', 'link-18');">read_seq_data</a></tt><tt class="py-op">(</tt><tt class="py-name">options</tt><tt class="py-op">.</tt><tt class="py-name">fin</tt><tt class="py-op">,</tt>  </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">            <tt class="py-name">options</tt><tt class="py-op">.</tt><tt class="py-name">input_parser</tt><tt class="py-op">.</tt><tt class="py-name">read</tt><tt class="py-op">,</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">            <tt class="py-name">alphabet</tt><tt class="py-op">=</tt><tt class="py-name">options</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">,</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">            <tt class="py-name">ignore_lower_case</tt> <tt class="py-op">=</tt> <tt class="py-name">options</tt><tt class="py-op">.</tt><tt class="py-name">ignore_lower_case</tt><tt class="py-op">)</tt>    </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line">             </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">options</tt><tt class="py-op">.</tt><tt class="py-name">reverse</tt><tt class="py-op">:</tt>  </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">            <tt class="py-name">seqs</tt> <tt class="py-op">=</tt> <tt class="py-name">SeqList</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">s</tt><tt class="py-op">.</tt><tt class="py-name">reverse</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">seqs</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">seqs</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">         </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">options</tt><tt class="py-op">.</tt><tt class="py-name">complement</tt> <tt class="py-op">:</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">            <tt class="py-name">seqs</tt><tt class="py-op">=</tt> <tt class="py-name">SeqList</tt><tt class="py-op">(</tt> <tt class="py-op">[</tt><tt class="py-name">Seq</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">,</tt><tt class="py-name">seqs</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">complement</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">seqs</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">seqs</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line"> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line">           </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">         </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">        <tt class="py-name">prior</tt> <tt class="py-op">=</tt> <tt class="py-name">parse_prior</tt><tt class="py-op">(</tt> <tt class="py-name">options</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Variable weblogolib._cgi.composition=weblogolib._cgi-module.html#composition"><a title="weblogolib._cgi.composition" class="py-name" href="#" onclick="return doclink('link-21', 'composition', 'link-21');">composition</a></tt><tt class="py-op">,</tt><tt class="py-name">seqs</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">,</tt> <tt class="py-name">options</tt><tt class="py-op">.</tt><tt class="py-name">weight</tt><tt class="py-op">)</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="weblogolib.LogoData" class="py-name" href="#" onclick="return doclink('link-22', 'LogoData', 'link-6');">LogoData</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Class Method weblogolib.LogoData.from_seqs()=weblogolib.LogoData-class.html#from_seqs"><a title="weblogolib.LogoData.from_seqs" class="py-name" href="#" onclick="return doclink('link-23', 'from_seqs', 'link-23');">from_seqs</a></tt><tt class="py-op">(</tt><tt class="py-name">seqs</tt><tt class="py-op">,</tt> <tt class="py-name">prior</tt><tt class="py-op">)</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line"> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">        <tt class="py-keyword">from</tt> <tt class="py-name">corebio</tt><tt class="py-op">.</tt><tt class="py-name">matrix</tt> <tt class="py-keyword">import</tt> <tt class="py-name">Motif</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">     </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">options</tt><tt class="py-op">.</tt><tt class="py-name">ignore_lower_case</tt><tt class="py-op">:</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"error: option --ignore-lower-case incompatible with matrix input"</tt><tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">         </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">        <tt class="py-comment">#FIXME : implement</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">if</tt> <tt class="py-name">options</tt><tt class="py-op">.</tt><tt class="py-name">reverse</tt><tt class="py-op">:</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"error: option --reverse incompatible with matrix input"</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">         </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">        <tt class="py-comment">#FIXME : implement</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">if</tt> <tt class="py-name">options</tt><tt class="py-op">.</tt><tt class="py-name">complement</tt><tt class="py-op">:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"error: option --complement incompatible with matrix input"</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">                       </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">        <tt class="py-name">motif</tt> <tt class="py-op">=</tt> <tt class="py-name">Motif</tt><tt class="py-op">.</tt><tt class="py-name">read_transfac</tt><tt class="py-op">(</tt><tt class="py-name">options</tt><tt class="py-op">.</tt><tt class="py-name">fin</tt><tt class="py-op">,</tt> <tt class="py-name">alphabet</tt><tt class="py-op">=</tt><tt class="py-name">options</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">        <tt class="py-name">prior</tt> <tt class="py-op">=</tt> <tt class="py-name">parse_prior</tt><tt class="py-op">(</tt> <tt class="py-name">options</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="weblogolib._cgi.composition" class="py-name" href="#" onclick="return doclink('link-24', 'composition', 'link-21');">composition</a></tt><tt class="py-op">,</tt><tt class="py-name">motif</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">,</tt> <tt class="py-name">options</tt><tt class="py-op">.</tt><tt class="py-name">weight</tt><tt class="py-op">)</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">        <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt id="link-25" class="py-name"><a title="weblogolib.LogoData" class="py-name" href="#" onclick="return doclink('link-25', 'LogoData', 'link-6');">LogoData</a></tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Class Method weblogolib.LogoData.from_counts()=weblogolib.LogoData-class.html#from_counts"><a title="weblogolib.LogoData.from_counts" class="py-name" href="#" onclick="return doclink('link-26', 'from_counts', 'link-26');">from_counts</a></tt><tt class="py-op">(</tt><tt class="py-name">motif</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">,</tt> <tt class="py-name">motif</tt><tt class="py-op">,</tt> <tt class="py-name">prior</tt><tt class="py-op">)</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">         </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">data</tt> </tt>
</div><a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">      </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">              </tt>
<a name="_build_logoformat"></a><div id="_build_logoformat-def"><a name="L168"></a><tt class="py-lineno">168</tt> <a class="py-toggle" href="#" id="_build_logoformat-toggle" onclick="return toggle('_build_logoformat');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib._cli-module.html#_build_logoformat">_build_logoformat</a><tt class="py-op">(</tt> <tt class="py-param">logodata</tt><tt class="py-op">,</tt> <tt class="py-param">opts</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="_build_logoformat-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_build_logoformat-expanded"><a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">    <tt class="py-docstring">""" Extract and process relevant option values and return a </tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line"><tt class="py-docstring">    LogoFormat object."""</tt>  </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line"> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line">    <tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt>   </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">    <tt class="py-name">direct_from_opts</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line">        <tt class="py-string">"stacks_per_line"</tt><tt class="py-op">,</tt>  </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">        <tt class="py-string">"logo_title"</tt><tt class="py-op">,</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line">        <tt class="py-string">"yaxis_label"</tt><tt class="py-op">,</tt>  </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">        <tt class="py-string">"show_xaxis"</tt><tt class="py-op">,</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line">        <tt class="py-string">"show_yaxis"</tt><tt class="py-op">,</tt>         </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">        <tt class="py-string">"xaxis_label"</tt><tt class="py-op">,</tt>  </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">        <tt class="py-string">"show_ends"</tt><tt class="py-op">,</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">        <tt class="py-string">"fineprint"</tt><tt class="py-op">,</tt>   </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">        <tt class="py-string">"show_errorbars"</tt><tt class="py-op">,</tt>  </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">        <tt class="py-string">"show_boxes"</tt><tt class="py-op">,</tt>   </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line">        <tt class="py-string">"yaxis_tic_interval"</tt><tt class="py-op">,</tt>  </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line">        <tt class="py-string">"resolution"</tt><tt class="py-op">,</tt>       </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">        <tt class="py-string">"alphabet"</tt><tt class="py-op">,</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">        <tt class="py-string">"debug"</tt><tt class="py-op">,</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">        <tt class="py-string">"show_ends"</tt><tt class="py-op">,</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">        <tt class="py-string">"default_color"</tt><tt class="py-op">,</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">        <tt class="py-comment">#"show_color_key",</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line">        <tt class="py-string">"color_scheme"</tt><tt class="py-op">,</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line">        <tt class="py-string">"unit_name"</tt><tt class="py-op">,</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line">        <tt class="py-string">"logo_label"</tt><tt class="py-op">,</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line">        <tt class="py-string">"yaxis_scale"</tt><tt class="py-op">,</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line">        <tt class="py-string">"first_index"</tt><tt class="py-op">,</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">        <tt class="py-string">"logo_start"</tt><tt class="py-op">,</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line">        <tt class="py-string">"logo_end"</tt><tt class="py-op">,</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">        <tt class="py-string">"scale_width"</tt><tt class="py-op">,</tt>  </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">        <tt class="py-string">"annotate"</tt><tt class="py-op">,</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line">        <tt class="py-string">"stack_width"</tt><tt class="py-op">,</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line">        <tt class="py-string">"stack_aspect_ratio"</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line">        <tt class="py-op">]</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">   </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">direct_from_opts</tt><tt class="py-op">:</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">        <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">opts</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line"> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line"><tt class="py-comment">#    logo_size = copy.copy(opts.__dict__['logo_size'])</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#    size_from_opts = ["stack_width", "stack_height"]</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#    for k in size_from_opts :</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#        length = getattr(opts, k)</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#        if length : setattr( logo_size, k, length )</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#   args["size"] = logo_size    </tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line"> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">opts</tt><tt class="py-op">.</tt><tt class="py-name">colors</tt><tt class="py-op">:</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line">        <tt class="py-name">color_scheme</tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name"><a title="weblogolib.colorscheme.ColorScheme" class="py-name" href="#" onclick="return doclink('link-27', 'ColorScheme', 'link-2');">ColorScheme</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-28" class="py-name"><a title="weblogolib.color
weblogolib.colorscheme.ColorScheme.color" class="py-name" href="#" onclick="return doclink('link-28', 'color', 'link-0');">color</a></tt><tt class="py-op">,</tt> <tt class="py-name">symbols</tt><tt class="py-op">,</tt> <tt class="py-name">desc</tt> <tt class="py-keyword">in</tt> <tt class="py-name">opts</tt><tt class="py-op">.</tt><tt class="py-name">colors</tt><tt class="py-op">:</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line">            <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line">                <tt class="py-comment">#c = Color.from_string(color)</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-name">color_scheme</tt><tt class="py-op">.</tt><tt class="py-name">groups</tt><tt class="py-op">.</tt><tt class="py-name">append</tt><tt class="py-op">(</tt> <tt id="link-29" class="py-name"><a title="weblogolib.colorscheme.ColorGroup" class="py-name" href="#" onclick="return doclink('link-29', 'ColorGroup', 'link-3');">ColorGroup</a></tt><tt class="py-op">(</tt><tt class="py-name">symbols</tt><tt class="py-op">,</tt> <tt id="link-30" class="py-name"><a title="weblogolib.color
weblogolib.colorscheme.ColorScheme.color" class="py-name" href="#" onclick="return doclink('link-30', 'color', 'link-0');">color</a></tt><tt class="py-op">,</tt> <tt class="py-name">desc</tt><tt class="py-op">)</tt>  <tt class="py-op">)</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line">            <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt> <tt class="py-op">:</tt>  </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line">                     <tt class="py-string">"error: option --color: invalid value: '%s'"</tt> <tt class="py-op">%</tt> <tt id="link-31" class="py-name"><a title="weblogolib.color
weblogolib.colorscheme.ColorScheme.color" class="py-name" href="#" onclick="return doclink('link-31', 'color', 'link-0');">color</a></tt> <tt class="py-op">)</tt>           </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">                  </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line">        <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-string">"color_scheme"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">color_scheme</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line">  </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line">  </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">opts</tt><tt class="py-op">.</tt><tt class="py-name">annotate</tt><tt class="py-op">:</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line">        <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-string">"annotate"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">opts</tt><tt class="py-op">.</tt><tt class="py-name">annotate</tt><tt class="py-op">.</tt><tt class="py-name">split</tt><tt class="py-op">(</tt><tt class="py-string">','</tt><tt class="py-op">)</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line">  </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line">     </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line">    <tt class="py-name">logooptions</tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name"><a title="weblogolib.LogoOptions" class="py-name" href="#" onclick="return doclink('link-32', 'LogoOptions', 'link-5');">LogoOptions</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt>  </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">a</tt><tt class="py-op">,</tt> <tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">args</tt><tt class="py-op">.</tt><tt class="py-name">iteritems</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">        <tt class="py-name">setattr</tt><tt class="py-op">(</tt><tt class="py-name">logooptions</tt><tt class="py-op">,</tt><tt class="py-name">a</tt><tt class="py-op">,</tt><tt class="py-name">v</tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line"> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line">     </tt>
<a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line">    <tt class="py-name">theformat</tt> <tt class="py-op">=</tt>  <tt id="link-33" class="py-name"><a title="weblogolib.LogoFormat" class="py-name" href="#" onclick="return doclink('link-33', 'LogoFormat', 'link-7');">LogoFormat</a></tt><tt class="py-op">(</tt><tt class="py-name">logodata</tt><tt class="py-op">,</tt> <tt class="py-name">logooptions</tt> <tt class="py-op">)</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">theformat</tt> </tt>
</div><a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line"> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line">     </tt>
<a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line">    </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line">     </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line">    </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line">     </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line"><tt class="py-comment"># ========================== OPTIONS ==========================</tt> </tt>
<a name="_build_option_parser"></a><div id="_build_option_parser-def"><a name="L246"></a><tt class="py-lineno">246</tt> <a class="py-toggle" href="#" id="_build_option_parser-toggle" onclick="return toggle('_build_option_parser');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="weblogolib._cli-module.html#_build_option_parser">_build_option_parser</a><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="_build_option_parser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_build_option_parser-expanded"><a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line">    <tt class="py-name">defaults</tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name"><a title="weblogolib.LogoOptions" class="py-name" href="#" onclick="return doclink('link-34', 'LogoOptions', 'link-5');">LogoOptions</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line">    <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt class="py-name">DeOptionParser</tt><tt class="py-op">(</tt><tt class="py-name">usage</tt><tt class="py-op">=</tt><tt class="py-string">"%prog [options]  &lt; sequence_data.fa &gt; sequence_logo.eps"</tt><tt class="py-op">,</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line">        <tt id="link-35" class="py-name"><a title="weblogolib.description" class="py-name" href="#" onclick="return doclink('link-35', 'description', 'link-9');">description</a></tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name"><a title="weblogolib.description" class="py-name" href="#" onclick="return doclink('link-36', 'description', 'link-9');">description</a></tt><tt class="py-op">,</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line">        <tt id="link-37" class="py-name" targets="Method weblogolib.GhostscriptAPI.version()=weblogolib.GhostscriptAPI-class.html#version"><a title="weblogolib.GhostscriptAPI.version" class="py-name" href="#" onclick="return doclink('link-37', 'version', 'link-37');">version</a></tt>     <tt class="py-op">=</tt> <tt id="link-38" class="py-name"><a title="weblogolib.release_description" class="py-name" href="#" onclick="return doclink('link-38', 'release_description', 'link-10');">release_description</a></tt><tt class="py-op">,</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line">        <tt class="py-name">add_verbose_options</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line">        <tt class="py-op">)</tt>     </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line">         </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line">    <tt class="py-name">io_grp</tt> <tt class="py-op">=</tt> <tt class="py-name">OptionGroup</tt><tt class="py-op">(</tt><tt class="py-name">parser</tt><tt class="py-op">,</tt> <tt class="py-string">"Input/Output Options"</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line">    <tt class="py-name">data_grp</tt> <tt class="py-op">=</tt> <tt class="py-name">OptionGroup</tt><tt class="py-op">(</tt><tt class="py-name">parser</tt><tt class="py-op">,</tt> <tt class="py-string">"Logo Data Options"</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line">    <tt class="py-name">trans_grp</tt> <tt class="py-op">=</tt> <tt class="py-name">OptionGroup</tt><tt class="py-op">(</tt><tt class="py-name">parser</tt><tt class="py-op">,</tt> <tt class="py-string">"Transformations"</tt><tt class="py-op">,</tt> <tt class="py-string">"Optional transformations of the sequence data."</tt><tt class="py-op">)</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line"> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line">  </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line">    <tt class="py-name">format_grp</tt> <tt class="py-op">=</tt> <tt class="py-name">OptionGroup</tt><tt class="py-op">(</tt><tt class="py-name">parser</tt><tt class="py-op">,</tt> <tt class="py-string">"Logo Format Options"</tt><tt class="py-op">,</tt>  </tt>
<a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line">        <tt class="py-string">"These options control the format and display of the logo."</tt><tt class="py-op">)</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line">    <tt class="py-name">color_grp</tt> <tt class="py-op">=</tt> <tt class="py-name">OptionGroup</tt><tt class="py-op">(</tt><tt class="py-name">parser</tt><tt class="py-op">,</tt> <tt class="py-string">"Color Options"</tt><tt class="py-op">,</tt>  </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line">        <tt class="py-string">"Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc."</tt><tt class="py-op">)</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line">    <tt class="py-name">advanced_grp</tt> <tt class="py-op">=</tt> <tt class="py-name">OptionGroup</tt><tt class="py-op">(</tt><tt class="py-name">parser</tt><tt class="py-op">,</tt> <tt class="py-string">"Advanced Format Options"</tt><tt class="py-op">,</tt>  </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line">        <tt class="py-string">"These options provide fine control over the display of the logo. "</tt><tt class="py-op">)</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line">    <tt class="py-name">server_grp</tt> <tt class="py-op">=</tt> <tt class="py-name">OptionGroup</tt><tt class="py-op">(</tt><tt class="py-name">parser</tt><tt class="py-op">,</tt> <tt class="py-string">"WebLogo Server"</tt><tt class="py-op">,</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line">        <tt class="py-string">"Run a standalone webserver on a local port."</tt><tt class="py-op">)</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line"> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line"> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">add_option_group</tt><tt class="py-op">(</tt><tt class="py-name">io_grp</tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">add_option_group</tt><tt class="py-op">(</tt><tt class="py-name">data_grp</tt><tt class="py-op">)</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">add_option_group</tt><tt class="py-op">(</tt><tt class="py-name">trans_grp</tt><tt class="py-op">)</tt>       </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">add_option_group</tt><tt class="py-op">(</tt><tt class="py-name">format_grp</tt><tt class="py-op">)</tt>   </tt>
<a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">add_option_group</tt><tt class="py-op">(</tt><tt class="py-name">color_grp</tt><tt class="py-op">)</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">add_option_group</tt><tt class="py-op">(</tt><tt class="py-name">advanced_grp</tt><tt class="py-op">)</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line">    <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt class="py-name">add_option_group</tt><tt class="py-op">(</tt><tt class="py-name">server_grp</tt><tt class="py-op">)</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line">     </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line">    <tt class="py-comment"># ========================== IO OPTIONS ==========================</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line"><tt class="py-comment"></tt>     </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line">    <tt class="py-name">io_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-f"</tt><tt class="py-op">,</tt> <tt class="py-string">"--fin"</tt><tt class="py-op">,</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"fin"</tt><tt class="py-op">,</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"file_in"</tt><tt class="py-op">,</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stdin</tt><tt class="py-op">,</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Sequence input file (default: stdin)"</tt><tt class="py-op">,</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"FILENAME"</tt><tt class="py-op">)</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line"> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line">    <tt class="py-comment"># Add position weight matrix formats to input parsers by hand</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">fin_choices</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-name">seq_io</tt><tt class="py-op">.</tt><tt class="py-name">format_names</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line">    <tt class="py-name">fin_choices</tt><tt class="py-op">[</tt><tt class="py-string">'transfac'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">'transfac'</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line">     </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line">    <tt class="py-name">io_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt><tt class="py-string">"-D"</tt><tt class="py-op">,</tt> <tt class="py-string">"--datatype"</tt><tt class="py-op">,</tt>  </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"input_parser"</tt><tt class="py-op">,</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> <tt class="py-name">type</tt> <tt class="py-op">=</tt><tt class="py-string">"dict"</tt><tt class="py-op">,</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt>  <tt class="py-line">        <tt class="py-name">default</tt> <tt class="py-op">=</tt> <tt class="py-name">seq_io</tt><tt class="py-op">,</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt>  <tt class="py-line">        <tt class="py-name">choices</tt> <tt class="py-op">=</tt> <tt class="py-name">fin_choices</tt><tt class="py-op">,</tt>       <tt class="py-comment"># seq_io.format_names(),</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Type of multiple sequence alignment or position weight matrix file: (%s, transfac)"</tt> <tt class="py-op">%</tt>  </tt>
<a name="L297"></a><tt class="py-lineno">297</tt>  <tt class="py-line">           <tt class="py-string">', '</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Static Method weblogolib.color.Color.names()=weblogolib.color.Color-class.html#names"><a title="weblogolib.color.Color.names" class="py-name" href="#" onclick="return doclink('link-39', 'names', 'link-39');">names</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">f</tt> <tt class="py-keyword">in</tt> <tt class="py-name">seq_io</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Variable weblogolib.GhostscriptAPI.formats=weblogolib.GhostscriptAPI-class.html#formats"><a title="weblogolib.GhostscriptAPI.formats" class="py-name" href="#" onclick="return doclink('link-40', 'formats', 'link-40');">formats</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"FORMAT"</tt><tt class="py-op">)</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt>  <tt class="py-line"> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt>  <tt class="py-line">    <tt class="py-name">io_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt><tt class="py-string">"-o"</tt><tt class="py-op">,</tt> <tt class="py-string">"--fout"</tt><tt class="py-op">,</tt> <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"fout"</tt><tt class="py-op">,</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"file_out"</tt><tt class="py-op">,</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stdout</tt><tt class="py-op">,</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Output file (default: stdout)"</tt><tt class="py-op">,</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"FILENAME"</tt><tt class="py-op">)</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line"> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt>  <tt class="py-line">    <tt class="py-name">io_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-F"</tt><tt class="py-op">,</tt> <tt class="py-string">"--format"</tt><tt class="py-op">,</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"formatter"</tt><tt class="py-op">,</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"dict"</tt><tt class="py-op">,</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt>  <tt class="py-line">        <tt class="py-name">choices</tt> <tt class="py-op">=</tt> <tt id="link-41" class="py-name"><a title="weblogolib.formatters" class="py-name" href="#" onclick="return doclink('link-41', 'formatters', 'link-11');">formatters</a></tt><tt class="py-op">,</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt> <tt class="py-string">"FORMAT"</tt><tt class="py-op">,</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Format of output: eps (default), png, png_print, pdf, jpeg, svg, logodata"</tt><tt class="py-op">,</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt>  <tt class="py-line">        <tt class="py-name">default</tt> <tt class="py-op">=</tt> <tt class="py-name">default_formatter</tt><tt class="py-op">)</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt>  <tt class="py-line"> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt>  <tt class="py-line"> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt>  <tt class="py-line">    <tt class="py-comment"># ========================== Data OPTIONS ==========================</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt>  <tt class="py-line"> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt>  <tt class="py-line">  </tt>
<a name="L320"></a><tt class="py-lineno">320</tt>  <tt class="py-line">    <tt class="py-name">data_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-A"</tt><tt class="py-op">,</tt> <tt class="py-string">"--sequence-type"</tt><tt class="py-op">,</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"alphabet"</tt><tt class="py-op">,</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"dict"</tt><tt class="py-op">,</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt>  <tt class="py-line">        <tt class="py-name">choices</tt> <tt class="py-op">=</tt> <tt id="link-42" class="py-name"><a title="weblogolib.std_alphabets" class="py-name" href="#" onclick="return doclink('link-42', 'std_alphabets', 'link-13');">std_alphabets</a></tt><tt class="py-op">,</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"The type of sequence data: 'protein', 'rna' or 'dna'."</tt><tt class="py-op">,</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"TYPE"</tt><tt class="py-op">)</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt>  <tt class="py-line">                        </tt>
<a name="L328"></a><tt class="py-lineno">328</tt>  <tt class="py-line">    <tt class="py-name">data_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-a"</tt><tt class="py-op">,</tt> <tt class="py-string">"--alphabet"</tt><tt class="py-op">,</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"alphabet"</tt><tt class="py-op">,</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"The set of symbols to count, e.g. 'AGTC'. "</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt>  <tt class="py-line">             <tt class="py-string">"All characters not in the alphabet are ignored. "</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt>  <tt class="py-line">             <tt class="py-string">"If neither the alphabet nor sequence-type are specified then weblogo will examine the input data and make an educated guess. "</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt>  <tt class="py-line">             <tt class="py-string">"See also --sequence-type, --ignore-lower-case"</tt> <tt class="py-op">)</tt>                        </tt>
<a name="L335"></a><tt class="py-lineno">335</tt>  <tt class="py-line">     </tt>
<a name="L336"></a><tt class="py-lineno">336</tt>  <tt class="py-line">        </tt>
<a name="L337"></a><tt class="py-lineno">337</tt>  <tt class="py-line">    <tt class="py-name">data_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-U"</tt><tt class="py-op">,</tt> <tt class="py-string">"--units"</tt><tt class="py-op">,</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"unit_name"</tt><tt class="py-op">,</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt>  <tt class="py-line">        <tt class="py-name">choices</tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name"><a title="weblogolib.std_units" class="py-name" href="#" onclick="return doclink('link-43', 'std_units', 'link-14');">std_units</a></tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt>     </tt>
<a name="L341"></a><tt class="py-lineno">341</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"choice"</tt><tt class="py-op">,</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt>  <tt class="py-line">        <tt class="py-name">default</tt> <tt class="py-op">=</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">unit_name</tt><tt class="py-op">,</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"A unit of entropy ('bits' (default), 'nats', 'digits'), or a unit of free energy ('kT', 'kJ/mol', 'kcal/mol'), or 'probability' for probabilities"</tt><tt class="py-op">,</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt> <tt class="py-op">=</tt> <tt class="py-string">"NUMBER"</tt><tt class="py-op">)</tt>  </tt>
<a name="L345"></a><tt class="py-lineno">345</tt>  <tt class="py-line"> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt>  <tt class="py-line"> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt>  <tt class="py-line">    <tt class="py-name">data_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--composition"</tt><tt class="py-op">,</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"composition"</tt><tt class="py-op">,</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"string"</tt><tt class="py-op">,</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt>  <tt class="py-line">        <tt class="py-name">default</tt> <tt class="py-op">=</tt> <tt class="py-string">"auto"</tt><tt class="py-op">,</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"The expected composition of the sequences: 'auto' (default), 'equiprobable', 'none' (do not perform any compositional adjustment), a CG percentage, a species name (e.g. 'E. coli', 'H. sapiens'), or an explicit distribution (e.g. \"{'A':10, 'C':40, 'G':40, 'T':10}\"). The automatic option uses a typical distribution for proteins and equiprobable distribution for everything else. "</tt><tt class="py-op">,</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"COMP."</tt><tt class="py-op">)</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt>  <tt class="py-line"> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt>  <tt class="py-line">    <tt class="py-name">data_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--weight"</tt><tt class="py-op">,</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"weight"</tt><tt class="py-op">,</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"float"</tt><tt class="py-op">,</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt>  <tt class="py-line">        <tt class="py-name">default</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"The weight of prior data.  Default: total pseudocounts equal to the number of monomer types."</tt><tt class="py-op">,</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"NUMBER"</tt><tt class="py-op">)</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt>  <tt class="py-line"> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt>  <tt class="py-line">    <tt class="py-name">data_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-i"</tt><tt class="py-op">,</tt> <tt class="py-string">"--first-index"</tt><tt class="py-op">,</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"first_index"</tt><tt class="py-op">,</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"int"</tt><tt class="py-op">,</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt>  <tt class="py-line">        <tt class="py-name">default</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Index of first position in sequence data (default: 1)"</tt><tt class="py-op">,</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"INDEX"</tt><tt class="py-op">)</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt>  <tt class="py-line"> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt>  <tt class="py-line">    <tt class="py-name">data_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-l"</tt><tt class="py-op">,</tt> <tt class="py-string">"--lower"</tt><tt class="py-op">,</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"logo_start"</tt><tt class="py-op">,</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"int"</tt><tt class="py-op">,</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Lower bound of sequence to display"</tt><tt class="py-op">,</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"INDEX"</tt><tt class="py-op">)</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt>  <tt class="py-line">     </tt>
<a name="L378"></a><tt class="py-lineno">378</tt>  <tt class="py-line">    <tt class="py-name">data_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-u"</tt><tt class="py-op">,</tt> <tt class="py-string">"--upper"</tt><tt class="py-op">,</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"logo_end"</tt><tt class="py-op">,</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"int"</tt><tt class="py-op">,</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Upper bound of sequence to display"</tt><tt class="py-op">,</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"INDEX"</tt><tt class="py-op">)</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt>  <tt class="py-line"> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt>  <tt class="py-line">    <tt class="py-comment"># ========================== Transformation OPTIONS ==========================</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt>  <tt class="py-line"><tt class="py-comment"></tt>     </tt>
<a name="L387"></a><tt class="py-lineno">387</tt>  <tt class="py-line"> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt>  <tt class="py-line">    <tt class="py-comment"># FIXME Add test? </tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">trans_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--ignore-lower-case"</tt><tt class="py-op">,</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"ignore_lower_case"</tt><tt class="py-op">,</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store_true"</tt><tt class="py-op">,</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Disregard lower case letters and only count upper case letters in sequences."</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt>  <tt class="py-line">       <tt class="py-op">)</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt>  <tt class="py-line"> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt>  <tt class="py-line">    <tt class="py-name">trans_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--reverse"</tt><tt class="py-op">,</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"reverse"</tt><tt class="py-op">,</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store_true"</tt><tt class="py-op">,</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"reverse sequences"</tt><tt class="py-op">,</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt>  <tt class="py-line">        <tt class="py-op">)</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt>  <tt class="py-line"> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt>  <tt class="py-line">    <tt class="py-name">trans_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--complement"</tt><tt class="py-op">,</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"complement"</tt><tt class="py-op">,</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store_true"</tt><tt class="py-op">,</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"complement DNA sequences"</tt><tt class="py-op">,</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt>  <tt class="py-line">        <tt class="py-op">)</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt>  <tt class="py-line">     </tt>
<a name="L410"></a><tt class="py-lineno">410</tt>  <tt class="py-line"> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt>  <tt class="py-line"> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt>  <tt class="py-line">    <tt class="py-comment"># ========================== FORMAT OPTIONS ==========================</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt>  <tt class="py-line">    <tt class="py-name">format_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-s"</tt><tt class="py-op">,</tt> <tt class="py-string">"--size"</tt><tt class="py-op">,</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"stack_width"</tt><tt class="py-op">,</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt>  <tt class="py-line">        <tt class="py-name">type</tt> <tt class="py-op">=</tt><tt class="py-string">"dict"</tt><tt class="py-op">,</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt>  <tt class="py-line">        <tt class="py-name">choices</tt> <tt class="py-op">=</tt> <tt id="link-44" class="py-name"><a title="weblogolib.std_sizes" class="py-name" href="#" onclick="return doclink('link-44', 'std_sizes', 'link-15');">std_sizes</a></tt><tt class="py-op">,</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt> <tt class="py-op">=</tt> <tt class="py-string">"LOGOSIZE"</tt><tt class="py-op">,</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt>  <tt class="py-line">        <tt class="py-name">default</tt> <tt class="py-op">=</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">stack_width</tt><tt class="py-op">,</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Specify a standard logo size (small, medium (default), large)"</tt> <tt class="py-op">)</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt>  <tt class="py-line">             </tt>
<a name="L423"></a><tt class="py-lineno">423</tt>  <tt class="py-line">    <tt class="py-name">format_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-n"</tt><tt class="py-op">,</tt> <tt class="py-string">"--stacks-per-line"</tt><tt class="py-op">,</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"stacks_per_line"</tt><tt class="py-op">,</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"int"</tt><tt class="py-op">,</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Maximum number of logo stacks per logo line. (default: %default)"</tt><tt class="py-op">,</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt>  <tt class="py-line">        <tt class="py-name">default</tt> <tt class="py-op">=</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">stacks_per_line</tt><tt class="py-op">,</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"COUNT"</tt><tt class="py-op">)</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt>  <tt class="py-line"> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt>  <tt class="py-line">    <tt class="py-name">format_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-t"</tt><tt class="py-op">,</tt> <tt class="py-string">"--title"</tt><tt class="py-op">,</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"logo_title"</tt><tt class="py-op">,</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"string"</tt><tt class="py-op">,</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Logo title text."</tt><tt class="py-op">,</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt>  <tt class="py-line">        <tt class="py-name">default</tt> <tt class="py-op">=</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">logo_title</tt><tt class="py-op">,</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"TEXT"</tt><tt class="py-op">)</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt>  <tt class="py-line"> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt>  <tt class="py-line">    <tt class="py-name">format_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--label"</tt><tt class="py-op">,</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"logo_label"</tt><tt class="py-op">,</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"string"</tt><tt class="py-op">,</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"A figure label, e.g. '2a'"</tt><tt class="py-op">,</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt>  <tt class="py-line">        <tt class="py-name">default</tt> <tt class="py-op">=</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">logo_label</tt><tt class="py-op">,</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"TEXT"</tt><tt class="py-op">)</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt>  <tt class="py-line"> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt>  <tt class="py-line">    <tt class="py-name">format_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-X"</tt><tt class="py-op">,</tt> <tt class="py-string">"--show-xaxis"</tt><tt class="py-op">,</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt>  <tt class="py-line">        <tt class="py-name">type</tt> <tt class="py-op">=</tt> <tt class="py-string">"boolean"</tt><tt class="py-op">,</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">show_xaxis</tt><tt class="py-op">,</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt> <tt class="py-op">=</tt> <tt class="py-string">"YES/NO"</tt><tt class="py-op">,</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Display sequence numbers along x-axis? (default: %default)"</tt><tt class="py-op">)</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt>  <tt class="py-line">                        </tt>
<a name="L454"></a><tt class="py-lineno">454</tt>  <tt class="py-line">    <tt class="py-name">format_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-x"</tt><tt class="py-op">,</tt> <tt class="py-string">"--xlabel"</tt><tt class="py-op">,</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"xaxis_label"</tt><tt class="py-op">,</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"string"</tt><tt class="py-op">,</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt>  <tt class="py-line">        <tt class="py-name">default</tt> <tt class="py-op">=</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">xaxis_label</tt><tt class="py-op">,</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"X-axis label"</tt><tt class="py-op">,</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"TEXT"</tt><tt class="py-op">)</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt>  <tt class="py-line"> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt>  <tt class="py-line">    <tt class="py-name">format_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--annotate"</tt><tt class="py-op">,</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt>  <tt class="py-line">            <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"annotate"</tt><tt class="py-op">,</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt>  <tt class="py-line">            <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt>  <tt class="py-line">            <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"string"</tt><tt class="py-op">,</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt>  <tt class="py-line">            <tt class="py-name">default</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt>  <tt class="py-line">            <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"A comma separated list of custom stack annotations, e.g. '1,3,4,5,6,7'.  Annotation list must be same length as sequences."</tt><tt class="py-op">,</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt>  <tt class="py-line">            <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"TEXT"</tt><tt class="py-op">)</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt>  <tt class="py-line"> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt>  <tt class="py-line">    <tt class="py-name">format_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-S"</tt><tt class="py-op">,</tt> <tt class="py-string">"--yaxis"</tt><tt class="py-op">,</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"yaxis_scale"</tt><tt class="py-op">,</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"float"</tt><tt class="py-op">,</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Height of yaxis in units. (Default: Maximum value with uninformative prior.)"</tt><tt class="py-op">,</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt> <tt class="py-op">=</tt> <tt class="py-string">"UNIT"</tt><tt class="py-op">)</tt>  </tt>
<a name="L476"></a><tt class="py-lineno">476</tt>  <tt class="py-line"> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt>  <tt class="py-line">    <tt class="py-name">format_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-Y"</tt><tt class="py-op">,</tt> <tt class="py-string">"--show-yaxis"</tt><tt class="py-op">,</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt>  <tt class="py-line">        <tt class="py-name">type</tt> <tt class="py-op">=</tt> <tt class="py-string">"boolean"</tt><tt class="py-op">,</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt>  <tt class="py-line">        <tt class="py-name">dest</tt> <tt class="py-op">=</tt> <tt class="py-string">"show_yaxis"</tt><tt class="py-op">,</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">show_yaxis</tt><tt class="py-op">,</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt> <tt class="py-op">=</tt> <tt class="py-string">"YES/NO"</tt><tt class="py-op">,</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Display entropy scale along y-axis? (default: %default)"</tt><tt class="py-op">)</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt>  <tt class="py-line"> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt>  <tt class="py-line">    <tt class="py-name">format_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-y"</tt><tt class="py-op">,</tt> <tt class="py-string">"--ylabel"</tt><tt class="py-op">,</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"yaxis_label"</tt><tt class="py-op">,</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"string"</tt><tt class="py-op">,</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Y-axis label (default depends on plot type and units)"</tt><tt class="py-op">,</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"TEXT"</tt><tt class="py-op">)</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt>  <tt class="py-line"> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt>  <tt class="py-line">    <tt class="py-name">format_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-E"</tt><tt class="py-op">,</tt> <tt class="py-string">"--show-ends"</tt><tt class="py-op">,</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt>  <tt class="py-line">        <tt class="py-name">type</tt> <tt class="py-op">=</tt> <tt class="py-string">"boolean"</tt><tt class="py-op">,</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">show_ends</tt><tt class="py-op">,</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt> <tt class="py-op">=</tt> <tt class="py-string">"YES/NO"</tt><tt class="py-op">,</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Label the ends of the sequence? (default: %default)"</tt><tt class="py-op">)</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt>  <tt class="py-line">         </tt>
<a name="L499"></a><tt class="py-lineno">499</tt>  <tt class="py-line">    <tt class="py-name">format_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-P"</tt><tt class="py-op">,</tt> <tt class="py-string">"--fineprint"</tt><tt class="py-op">,</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"fineprint"</tt><tt class="py-op">,</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"string"</tt><tt class="py-op">,</tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">fineprint</tt><tt class="py-op">,</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"The fine print (default: weblogo version)"</tt><tt class="py-op">,</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"TEXT"</tt><tt class="py-op">)</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt>  <tt class="py-line"> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt>  <tt class="py-line">    <tt class="py-name">format_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--ticmarks"</tt><tt class="py-op">,</tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"yaxis_tic_interval"</tt><tt class="py-op">,</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"float"</tt><tt class="py-op">,</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">yaxis_tic_interval</tt><tt class="py-op">,</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Distance between ticmarks (default: %default)"</tt><tt class="py-op">,</tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt> <tt class="py-op">=</tt> <tt class="py-string">"NUMBER"</tt><tt class="py-op">)</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt>  <tt class="py-line"> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt>  <tt class="py-line">         </tt>
<a name="L516"></a><tt class="py-lineno">516</tt>  <tt class="py-line">    <tt class="py-name">format_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--errorbars"</tt><tt class="py-op">,</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt>  <tt class="py-line">        <tt class="py-name">dest</tt> <tt class="py-op">=</tt> <tt class="py-string">"show_errorbars"</tt><tt class="py-op">,</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt>  <tt class="py-line">        <tt class="py-name">type</tt> <tt class="py-op">=</tt> <tt class="py-string">"boolean"</tt><tt class="py-op">,</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">show_errorbars</tt><tt class="py-op">,</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt> <tt class="py-op">=</tt> <tt class="py-string">"YES/NO"</tt><tt class="py-op">,</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Display error bars? (default: %default)"</tt><tt class="py-op">)</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt>  <tt class="py-line">      </tt>
<a name="L524"></a><tt class="py-lineno">524</tt>  <tt class="py-line">        </tt>
<a name="L525"></a><tt class="py-lineno">525</tt>  <tt class="py-line">         </tt>
<a name="L526"></a><tt class="py-lineno">526</tt>  <tt class="py-line">    <tt class="py-comment"># ========================== Color OPTIONS ==========================</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment"># TODO: Future Feature</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment"># color_grp.add_option( "-K", "--color-key",</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#    dest= "show_color_key",</tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#    action="store",</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#    type = "boolean",</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#    default= defaults.show_color_key,</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#    metavar = "YES/NO",</tt> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#    help="Display a color key (default: %default)")</tt> </tt>
<a name="L535"></a><tt class="py-lineno">535</tt>  <tt class="py-line"><tt class="py-comment"></tt>         </tt>
<a name="L536"></a><tt class="py-lineno">536</tt>  <tt class="py-line">         </tt>
<a name="L537"></a><tt class="py-lineno">537</tt>  <tt class="py-line">    <tt class="py-name">color_scheme_choices</tt> <tt class="py-op">=</tt> <tt id="link-45" class="py-name"><a title="weblogolib.std_color_schemes" class="py-name" href="#" onclick="return doclink('link-45', 'std_color_schemes', 'link-16');">std_color_schemes</a></tt><tt class="py-op">.</tt><tt class="py-name">keys</tt><tt class="py-op">(</tt><tt class="py-op">)</tt>     </tt>
<a name="L538"></a><tt class="py-lineno">538</tt>  <tt class="py-line">    <tt class="py-name">color_scheme_choices</tt><tt class="py-op">.</tt><tt class="py-name">sort</tt><tt class="py-op">(</tt><tt class="py-op">)</tt>     </tt>
<a name="L539"></a><tt class="py-lineno">539</tt>  <tt class="py-line">    <tt class="py-name">color_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-c"</tt><tt class="py-op">,</tt> <tt class="py-string">"--color-scheme"</tt><tt class="py-op">,</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"color_scheme"</tt><tt class="py-op">,</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt>  <tt class="py-line">        <tt class="py-name">type</tt> <tt class="py-op">=</tt><tt class="py-string">"dict"</tt><tt class="py-op">,</tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt>  <tt class="py-line">        <tt class="py-name">choices</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name"><a title="weblogolib.std_color_schemes" class="py-name" href="#" onclick="return doclink('link-46', 'std_color_schemes', 'link-16');">std_color_schemes</a></tt><tt class="py-op">,</tt> </tt>
<a name="L544"></a><tt class="py-lineno">544</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt> <tt class="py-op">=</tt> <tt class="py-string">"SCHEME"</tt><tt class="py-op">,</tt> </tt>
<a name="L545"></a><tt class="py-lineno">545</tt>  <tt class="py-line">        <tt class="py-name">default</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-comment"># Auto</tt> </tt>
<a name="L546"></a><tt class="py-lineno">546</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Specify a standard color scheme (%s)"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L547"></a><tt class="py-lineno">547</tt>  <tt class="py-line">            <tt class="py-string">", "</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">color_scheme_choices</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt>  <tt class="py-line">             </tt>
<a name="L549"></a><tt class="py-lineno">549</tt>  <tt class="py-line">    <tt class="py-name">color_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-C"</tt><tt class="py-op">,</tt> <tt class="py-string">"--color"</tt><tt class="py-op">,</tt> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"colors"</tt><tt class="py-op">,</tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"append"</tt><tt class="py-op">,</tt> </tt>
<a name="L552"></a><tt class="py-lineno">552</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"COLOR SYMBOLS DESCRIPTION "</tt><tt class="py-op">,</tt> </tt>
<a name="L553"></a><tt class="py-lineno">553</tt>  <tt class="py-line">        <tt class="py-name">nargs</tt> <tt class="py-op">=</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> </tt>
<a name="L554"></a><tt class="py-lineno">554</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L555"></a><tt class="py-lineno">555</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Specify symbol colors, e.g. --color black AG 'Purine' --color red TC 'Pyrimidine' "</tt><tt class="py-op">)</tt>     </tt>
<a name="L556"></a><tt class="py-lineno">556</tt>  <tt class="py-line"> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt>  <tt class="py-line">    <tt class="py-name">color_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--default-color"</tt><tt class="py-op">,</tt> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"default_color"</tt><tt class="py-op">,</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L560"></a><tt class="py-lineno">560</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"COLOR"</tt><tt class="py-op">,</tt> </tt>
<a name="L561"></a><tt class="py-lineno">561</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">default_color</tt><tt class="py-op">,</tt> </tt>
<a name="L562"></a><tt class="py-lineno">562</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Symbol color if not otherwise specified."</tt><tt class="py-op">)</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt>  <tt class="py-line"> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt>  <tt class="py-line"> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt>  <tt class="py-line">    <tt class="py-comment"># ========================== Advanced options =========================   </tt> </tt>
<a name="L566"></a><tt class="py-lineno">566</tt>  <tt class="py-line"><tt class="py-comment"></tt>                 </tt>
<a name="L567"></a><tt class="py-lineno">567</tt>  <tt class="py-line">    <tt class="py-name">advanced_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">"-W"</tt><tt class="py-op">,</tt> <tt class="py-string">"--stack-width"</tt><tt class="py-op">,</tt> </tt>
<a name="L568"></a><tt class="py-lineno">568</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"stack_width"</tt><tt class="py-op">,</tt> </tt>
<a name="L569"></a><tt class="py-lineno">569</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L570"></a><tt class="py-lineno">570</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"float"</tt><tt class="py-op">,</tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">stack_width</tt><tt class="py-op">,</tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Width of a logo stack (default: %s)"</tt><tt class="py-op">%</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">stack_width</tt><tt class="py-op">,</tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"POINTS"</tt> <tt class="py-op">)</tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</tt>  <tt class="py-line"> </tt>
<a name="L575"></a><tt class="py-lineno">575</tt>  <tt class="py-line">    <tt class="py-name">advanced_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--aspect-ratio"</tt><tt class="py-op">,</tt> </tt>
<a name="L576"></a><tt class="py-lineno">576</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"stack_aspect_ratio"</tt><tt class="py-op">,</tt> </tt>
<a name="L577"></a><tt class="py-lineno">577</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"float"</tt><tt class="py-op">,</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">stack_aspect_ratio</tt> <tt class="py-op">,</tt> </tt>
<a name="L580"></a><tt class="py-lineno">580</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Ratio of stack height to width (default: %s)"</tt><tt class="py-op">%</tt><tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">stack_aspect_ratio</tt><tt class="py-op">,</tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"POINTS"</tt> <tt class="py-op">)</tt>     </tt>
<a name="L582"></a><tt class="py-lineno">582</tt>  <tt class="py-line"> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt>  <tt class="py-line">    <tt class="py-name">advanced_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--box"</tt><tt class="py-op">,</tt> </tt>
<a name="L584"></a><tt class="py-lineno">584</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"show_boxes"</tt><tt class="py-op">,</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L586"></a><tt class="py-lineno">586</tt>  <tt class="py-line">        <tt class="py-name">type</tt> <tt class="py-op">=</tt> <tt class="py-string">"boolean"</tt><tt class="py-op">,</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt>  </tt>
<a name="L588"></a><tt class="py-lineno">588</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt> <tt class="py-op">=</tt> <tt class="py-string">"YES/NO"</tt><tt class="py-op">,</tt> </tt>
<a name="L589"></a><tt class="py-lineno">589</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Draw boxes around symbols? (default: no)"</tt><tt class="py-op">)</tt> </tt>
<a name="L590"></a><tt class="py-lineno">590</tt>  <tt class="py-line"> </tt>
<a name="L591"></a><tt class="py-lineno">591</tt>  <tt class="py-line">    <tt class="py-name">advanced_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--resolution"</tt><tt class="py-op">,</tt> </tt>
<a name="L592"></a><tt class="py-lineno">592</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"resolution"</tt><tt class="py-op">,</tt> </tt>
<a name="L593"></a><tt class="py-lineno">593</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"float"</tt><tt class="py-op">,</tt> </tt>
<a name="L595"></a><tt class="py-lineno">595</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt><tt class="py-number">96</tt><tt class="py-op">,</tt> </tt>
<a name="L596"></a><tt class="py-lineno">596</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Bitmap resolution in dots per inch (DPI).  (Default: 96 DPI, except png_print, 600 DPI) Low resolution bitmaps (DPI&lt;300) are antialiased."</tt><tt class="py-op">,</tt> </tt>
<a name="L597"></a><tt class="py-lineno">597</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"DPI"</tt><tt class="py-op">)</tt>   </tt>
<a name="L598"></a><tt class="py-lineno">598</tt>  <tt class="py-line"> </tt>
<a name="L599"></a><tt class="py-lineno">599</tt>  <tt class="py-line">    <tt class="py-name">advanced_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--scale-width"</tt><tt class="py-op">,</tt> </tt>
<a name="L600"></a><tt class="py-lineno">600</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"scale_width"</tt><tt class="py-op">,</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L602"></a><tt class="py-lineno">602</tt>  <tt class="py-line">        <tt class="py-name">type</tt> <tt class="py-op">=</tt> <tt class="py-string">"boolean"</tt><tt class="py-op">,</tt> </tt>
<a name="L603"></a><tt class="py-lineno">603</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt> <tt class="py-name">True</tt><tt class="py-op">,</tt>  </tt>
<a name="L604"></a><tt class="py-lineno">604</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt> <tt class="py-op">=</tt> <tt class="py-string">"YES/NO"</tt><tt class="py-op">,</tt> </tt>
<a name="L605"></a><tt class="py-lineno">605</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Scale the visible stack width by the fraction of symbols in the column?  (I.e. columns with many gaps of unknowns are narrow.)  (Default: yes)"</tt><tt class="py-op">)</tt> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt>  <tt class="py-line">    </tt>
<a name="L607"></a><tt class="py-lineno">607</tt>  <tt class="py-line">    <tt class="py-name">advanced_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--debug"</tt><tt class="py-op">,</tt> </tt>
<a name="L608"></a><tt class="py-lineno">608</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L609"></a><tt class="py-lineno">609</tt>  <tt class="py-line">        <tt class="py-name">type</tt> <tt class="py-op">=</tt> <tt class="py-string">"boolean"</tt><tt class="py-op">,</tt> </tt>
<a name="L610"></a><tt class="py-lineno">610</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt> <tt class="py-name">defaults</tt><tt class="py-op">.</tt><tt class="py-name">debug</tt><tt class="py-op">,</tt> </tt>
<a name="L611"></a><tt class="py-lineno">611</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt> <tt class="py-op">=</tt> <tt class="py-string">"YES/NO"</tt><tt class="py-op">,</tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Output additional diagnostic information. (Default: %default)"</tt><tt class="py-op">)</tt> </tt>
<a name="L613"></a><tt class="py-lineno">613</tt>  <tt class="py-line"> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt>  <tt class="py-line"> </tt>
<a name="L615"></a><tt class="py-lineno">615</tt>  <tt class="py-line">    <tt class="py-comment"># ========================== Server options =========================   </tt> </tt>
<a name="L616"></a><tt class="py-lineno">616</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">server_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--serve"</tt><tt class="py-op">,</tt> </tt>
<a name="L617"></a><tt class="py-lineno">617</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"serve"</tt><tt class="py-op">,</tt> </tt>
<a name="L618"></a><tt class="py-lineno">618</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store_true"</tt><tt class="py-op">,</tt> </tt>
<a name="L619"></a><tt class="py-lineno">619</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt> <tt class="py-name">False</tt><tt class="py-op">,</tt> </tt>
<a name="L620"></a><tt class="py-lineno">620</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Start a standalone WebLogo server for creating sequence logos."</tt><tt class="py-op">)</tt>     </tt>
<a name="L621"></a><tt class="py-lineno">621</tt>  <tt class="py-line">     </tt>
<a name="L622"></a><tt class="py-lineno">622</tt>  <tt class="py-line">    <tt class="py-name">server_grp</tt><tt class="py-op">.</tt><tt class="py-name">add_option</tt><tt class="py-op">(</tt> <tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-string">"--port"</tt><tt class="py-op">,</tt> </tt>
<a name="L623"></a><tt class="py-lineno">623</tt>  <tt class="py-line">        <tt class="py-name">dest</tt><tt class="py-op">=</tt><tt class="py-string">"port"</tt><tt class="py-op">,</tt> </tt>
<a name="L624"></a><tt class="py-lineno">624</tt>  <tt class="py-line">        <tt class="py-name">action</tt><tt class="py-op">=</tt><tt class="py-string">"store"</tt><tt class="py-op">,</tt> </tt>
<a name="L625"></a><tt class="py-lineno">625</tt>  <tt class="py-line">        <tt class="py-name">type</tt><tt class="py-op">=</tt><tt class="py-string">"int"</tt><tt class="py-op">,</tt> </tt>
<a name="L626"></a><tt class="py-lineno">626</tt>  <tt class="py-line">        <tt class="py-name">default</tt><tt class="py-op">=</tt> <tt class="py-number">8080</tt><tt class="py-op">,</tt> </tt>
<a name="L627"></a><tt class="py-lineno">627</tt>  <tt class="py-line">        <tt class="py-name">help</tt><tt class="py-op">=</tt><tt class="py-string">"Listen to this local port. (Default: %default)"</tt><tt class="py-op">,</tt> </tt>
<a name="L628"></a><tt class="py-lineno">628</tt>  <tt class="py-line">        <tt class="py-name">metavar</tt><tt class="py-op">=</tt><tt class="py-string">"PORT"</tt><tt class="py-op">)</tt> </tt>
<a name="L629"></a><tt class="py-lineno">629</tt>  <tt class="py-line"> </tt>
<a name="L630"></a><tt class="py-lineno">630</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">parser</tt> </tt>
</div><a name="L631"></a><tt class="py-lineno">631</tt>  <tt class="py-line">     </tt>
<a name="L632"></a><tt class="py-lineno">632</tt>  <tt class="py-line">    <tt class="py-comment"># END _build_option_parser</tt> </tt>
<a name="L633"></a><tt class="py-lineno">633</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L634"></a><tt class="py-lineno">634</tt>  <tt class="py-line"> </tt>
<a name="L635"></a><tt class="py-lineno">635</tt>  <tt class="py-line"><tt class="py-comment">##############################################################</tt> </tt>
<a name="L636"></a><tt class="py-lineno">636</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt><script type="text/javascript">
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</pre>
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